Complete sequences of authentic feline mitochondrial (mt) DNA (17,009 base pairs) and mtDNA fragments transposed into a specific chromosome site (7,946 base pairs) were determined as an approach to elucidating the molecular aspects of gene transposition, gene amplification, and mtDNA evolution. Comparison of the two types of mtDNA sequences has provided useful information on the types and extent of mutations and the rate of mutation. These analyses revealed a relatively low amount of sequence divergence (5.1%) between these two types of mtDNAs, indicating recent integration and amplification of mtDNA in a chromosomal DNA within the last three million years. Dinucleotide repeats, d(CA)n, which are located in the breakpoint of the nuclear mtDNA, may suggest the involvement of these repeats in recombination and integration of nuclear mtDNA. Complete cat mtDNA sequence also showed the typical organization, codon usage and base composition of previously characterized mammalian mtDNAs, suggesting structural conservation of mammalian mtDNA.